VARIATION IN STRUTURE OF

CHROMOSOME
Chromosomal Aberrations
The somatic (2n) and gametic (n) chromosome numbers of a species
ordinarily remain constant.
This is due to the extremely precise mitotic and meiotic cell division.

Somatic cells of a diploid species contain two copies of each

chromosome, which are called homologous chromosome. Their
gametes, therefore contain only one copy of each chromosome, that
is they contain one chromosome complement or genome.

Each chromosome of a genome contains a definite numbers and

kinds of genes, which are arranged in a definite sequence.

Sometime due to mutation or spontaneous (without any known

causal factors), variation in chromosomal number or structure do
arise in nature. - Chromosomal aberrations.

Chromosomal aberration may be grouped into two broad

classes:
1. Structural 2. Numerical
Structural Chromosomal Aberrations
Chromosome structure variations result from chromosome breakage.
Broken chromosomes tend to re-join; if there is more than one break,
rejoining occurs at random and not necessarily with the correct ends.
The result is structural changes in the chromosomes.

Chromosome breakage is caused by X-rays, various chemicals, and can

also occur spontaneously.

There are four common type of structural aberrations:

1. Deletion or Deficiency
2. Duplication or Repeat
3. Inversion
4. Translocation.
Consider a normal chromosome with genes in alphabetical
order: a b c d e f g h i

1. Deletion: part of the chromosome has been removed:

abcghi

2. Dupliction: part of the chromosome is duplicated:

abcdefdefghi

3. Inversion: part of the chromosome has been re-

inserted in a reverse order: a b c f e d g h i
ring: the ends of the chromosome are joined together to
make a ring

4. translocation: parts of two non-homologous chromosomes are

joined:
If one normal chromosome is a b c d e f g h i and the other
chromosome is u v w x y z,
then a translocation between them would be
a b c d e f x y z and u v w g h i.
 Chromosome Structural Changes

There are 4 types of

chromosome structural
changes – all of them
associated with human
disorders
Deletion or deficiency
Loss of a chromosome segment is known as deletion or
deficiency , It can be terminal deletion or interstitial or intercalary
deletion

A single break near the end of the chromosome would be expected to

result in terminal deficiency.
If two breaks occur, a section may be deleted and an intercalary
deficiency created.

Terminal deficiencies might seem less complicated. But majority of

deficiencies detected are intercalary type within the chromosome.
Deletion was the first structural aberration detected by Bridges in 1917
from his genetic studies on X chromosome of Drosophila.

Deletion generally produce striking genetic and physiological effects.

When homozygous, most deletions are lethal, because most genes
are necessary for life and a homozygous deletion would have zero
copies of some genes.
Deletion in Prokaryotes
Deletions are found in prokaryotes as well, e.g., E.coli, T4
phage and Lambda phage.
In E.coli, deletions of up to 1 % of the bacterial chromosome are
known.
In lambda phage, however 20% of the genome may be missing in some
of the deletions.

Deletion in Human
Chromosome deletions are usually lethal even as heterozygotes,
resulting in zygotic loss, stillbirths, or infant death.
Sometimes, infants with small chromosome deficiencies however,
survive long enough to permit the abnormal phenotype they
express.
Cri-du-chat (Cat cry syndrome):
The name of the syndrome came from a cat-like mewing cry from
small weak infants with the disorder.
Other characteristics are microcephaly (small head), broad face and
saddle nose, physical and mental retardation.
Cri-du-chat patients die in infancy or early childhood.
The chromosome deficiency is in the short arm of chromosome 5 .

A Boy with Cri-du-Chat Syndrome –

a Debilitating Disorder Caused by Chromosome Deletion

Myelocytic leukemia
Another human disorder that is associated with a chromosome
abnormality is chronic myelocytic leukemia.
A deletion of chromosome 22 was described by P.C.Nowell and
Hungerford and was called “Philadelphia” (Ph’) chromosome after the
city in which the discovery was made.
Duplication
The presence of an additional chromosome segment, as compared to
that normally present in a nucleus is known as Duplication.
In a diploid organism, presence of a chromosome segment in more
than two copies per nucleus is called duplication.
Four types of duplication:
1. Tandem duplication
2. Reverse tandem duplication
3. Displaced duplication
4. Translocation duplication

The extra chromosome segment may be located immediately after the

normal segment in precisely the same orientation forms the tandem
When the gene sequence in the extra segment of a tandem in the
reverse order i.e, inverted , it is known as reverse tandem duplication
In some cases, the extra segment may be located in the same
chromosome but away from the normal segment – termed as
displaced duplication
The additional chromosome segment is located in a non-homologous
chromosome is translocation duplication.
Origin
Origin of duplication involves chromosome breakage and reunion of
chromosome segment with its homologous chromosome.
As a result, one of the two homologous involved in the production of a
duplication ends up with a deficiency, while the other has a
duplication for the concerned segment.
Another phenomenon, known as unequal crossing over, also leads to
exactly the same consequences for small chromosome segments.
For e.g., duplication of the band 16A of X chromosome of Drosophila
produces Bar eye.
This duplication is believed to originate due to unequal crossing over
between the two normal X chromosomes of female.
Inversion
When a segment of chromosome is oriented in the reverse direction,
such segment said to be inverted and the phenomenon is termed as
inversion.
The existence of inversion was first detected by Strutevant and
Plunkett in 1926.
Inversion occur when parts of chromosomes become detached , turn
through 180 degree and are reinserted in such a way that the genes
are in reversed order.

For example, a certain segment may be broken in two places, and the
breaks may be in close proximity because of chance loop in the
chromosome, When they rejoin, the wrong ends may become
connected.
The part on one side of the loop connects with broken end different
from the one with which it was formerly connected.
This leaves the other two broken ends to become attached.
The part within the loop thus becomes turned around or inverted.
Inversion may be classified into two types:
Pericentric - includes the centromere
Paracentric - does not include the centromere

In natural populations, pericentric inversions are much less frequent than

paracentric inversions.
In many sp, however, pericentric inversions are relatively common, e.g.,
in some grasshoppers.
Paracentric inversions appear to be very frequent in natural populations
of Drosophila.
Translocation
Integration of a chromosome segment into a nonhomologous
chromosome is known as translocation.
Three types:
1. simple translocation
2. shift
3. reciprocal translocation.

Simple translocation: In this case, terminal segment of a

chromosome is integrated at one end of a non-homologous region.
Simple translocations are rather rare.
Shift: In shift, an intercalary segment of a chromosome is integrated
within a non-homologous chromosome. Such translocations are
known in the populations of Drosophila, Neurospora etc.
Reciprocal translocation: It is produced when two non-homologous
chromosomes exchange segments – i.e., segments reciprocally
transferred.
Translocation of this type is most common
Translocations Lead to a Number of Human Cancers
In Burkitt’s lymphoma, a chromosome translocation causes a cell cycle-
promoting gene to always be active
Non-Disjunction
Generally during gametogenesis the homologous chromosomes of each pair
separate out (disjunction) and are equally distributed in the daughter cells.
But sometime there is an unequal distribution of chromosomes in the daughter
cells.
The failure of separation of homologous chromosome is called non disjunction.
This can occur either during mitosis or meiosis or embryogenesis.
Mitotic non-disjunction:
The failure of separation of homologous chromosomes during
mitosis is called mitotic non-disjunction.
May happen during first or second cleavage.
Here, one blastomere will receive 45 chromosomes, while other
will receive 47.

Meiotic non-disjunction:
The failure of separation of homologous chromosomes during
meiosis is called meiotic non-disjunction
Occurs during gametogensis
Here, one type contain 22 chromosome, while other will be 24.
Translocational Down Syndrome

Most cases of Down syndrome, trisomy-21,

are spontaneous. They are caused by non-
disjunction which gives an egg or sperm with
two copies of chromosome 21.
However, about 5% of Down’s cases are
caused by a translocation between
chromosome 21 and chromosome 14. These
translocational Down’s cases are heritable:
several children in the same family can have
the disease.

Sometimes a translocation occurs that joins the long arms together on one
centromere and the short arms on another centromere. In this case the short
arm chromosome is usually lost. The individual thus has a normal
chromosome 14, a normal chromosome 21, and a translocation chromosome,
called t(14;21).
During meiosis, one possible gamete that occurs has both the normal 21 and
the t(14;21) in it. When fertilized, the resulting zygote has 2 copies of the
important parts of chromosome 14, but 3 copies of chromosome 21: 2 normal
copies plus the long arm on the translocation. This zygote develops into a
person with Down syndrome.
Variation in chromosome number
Organism with one complete set of chromosomes is said to be euploid
(applies to haploid and diploid organisms).

Aneuploidy - variation in the number of individual chromosomes (but

not the total number of sets of chromosomes).

The discovery of aneuploidy dates back to 1916 when Bridges

discovered XO male and XXY female Drosophila, which had 7 and 9
chromosomes respectively, instead of normal 8.

Uses of Aneuploidy
They have been used to determine the phenotypic effect of loss or
gain of different chromosome
Used to produce chromosome substitution lines. Such lines yield
information on the effects of different chromosomes of a variety in the
same genetic background.
More about Aneuploidy

Nullisomy - loss of one

homologous chromosome
pair. (e.g., Oat )
Monosomy – loss of a
single chromosome
(Maize).
Trisomy - one extra
chromosome. (Datura)
Tetrasomy - one extra
chromosome pair.
Trisomy in Humans
Down Syndrome
The best known and most common chromosome related syndrome.
Formerly known as “Mongolism”
1866, when a physician named John Langdon Down published an essay in
England in which he described a set of children with common features who
were distinct from other children with mental retardation he referred to as
“Mongoloids.”
One child in every 800-1000 births has Down syndrome
250,000 in US has Down syndrome.
The cost and maintaining Down syndrome case in US is estimated at $ 1 billion
per year.

Patients having Down syndrome will Short in stature (four feet tall) and had
an epicanthal fold, broad short skulls, wild nostrils, large tongue, stubby
hands
Some babies may have short necks, small hands, and short fingers.
They are characterized as low in mentality.
Down syndrome results if the extra chromosome is number 21.
Amniocentesis for Detecting Aneuploidy

Chromosomal abnormalities are sufficiently well understood to permit

genetic counseling.
A fetus may be checked in early stages of development by
karyotyping the cultured cells obtained by a process called
amniocentesis.
A sample of fluid will taken from mother and fetal cells are cultured
and after a period of two to three weeks, chromosomes in dividing
cells can be stained and observed.
If three No.21 chromosomes are present, Down syndrome confirmed.

The risk for mothers less than 25 years of age to have the trisomy is
about 1 in 1500 births.
At 40 years of age, 1 in 100 births
At 45 years 1 in 40 births.
Patau syndrome
Chromosome Nomenclature: 47, +13
Chromosome formula: 2n+1
Clinical Syndrome: Trisomy-13
Estimated Frequency Birth: 1/20,000
Main Phenotypic Characteristics:
Mental deficiency and deafness, minor muscle seizures,
cleft lip, cardiac anomalies

Edwards syndrome
Chromosome Nomenclature: 47, +18
Chromosome formula: 2n+1
Clinical Syndrome: Trisomy-18
Estimated Frequency Birth: 1/8,000
Main Phenotypic Characteristics:
Multiple congenital malformation of many organs,
malformed ears, small mouth and nose with general elfin
appearance.
90% die in the first 6 months.
Turner syndrome
Chromosome Nomenclature: 45, X
Chromosome formula: 2n - 1
Clinical Syndrome: Turner
Estimated Frequency Birth: 1/2,500 female
Main Phenotypic Characteristics:
Female with retarded sexual development, usually sterile,
short stature, webbing of skin in neck region, cardiovascular
abnormalities, hearing impairment.

Klinefelter Syndromes
Chromosome Nomenclature: 47, XXY
Chromosome formula: 2n+1
Clinical Syndrome: Klinefelter
Estimated Frequency Birth: 1/500 male borth
Main Phenotypic Characteristics:
Pitched voice, Male, subfertile with small testes, developed
breasts, feminine, long limbs.
DNA Replication

2007-2008
DNA replication
DNA Replication is the process in
which the DNA within a cell makes
an exact copy of itself.

The four standard phases of a

eukaryotic cell
DNA replication occurring at S
Phase (DNA synthesis phase)

base pairing allows each strand to

serve as a template for a new
strand
new strand is 1/2 parent template
&
1/2 new DNA
The Three Possible DNA Replication Models
Conservative- would leave the
original strand intact and copy it.

Dispersive-would produce two DNA

molecule with sections of both old
and new along each strand.

Semiconservative –would produce

DNA molecule with both one old
strand and one new strand.

Semiconservative model: The dea

was presented by Watson & Crick
The two strands of the parental
molecule separate, and each acts
as a template for a new
complementary strand
New DNA consists of 1 PARENTAL
(original) and 1 NEW strand of DNA
BACTERIAL REPLICATION
DNA synthesis begins at a site termed the origin of replication
Each bacterial chromosome has only one
Synthesis of DNA proceeds bidirectionally around the bacterial chromosome
eventually meeting at the opposite side of the bacterial chromosome where
replication ends
The origin of replication in E. coli is
termed oriC
origin of Chromosomal replication
Important DNA sequences in oriC
AT-rich region
DnaA boxes

Replication begins with double-helix

denaturing into single-strands thus
exposing the bases.
Exposes a replication bubble from
which replication proceeds in both
directions.
Replication of circular DNA in E. coli :

Two replication forks result in a

theta-like () structure.

As strands separate, positive

supercoils form elsewhere in
the molecule.

Topoisomerases relieve tensions

in the supercoils, allowing the
DNA to continue to separate.
How can entire chromosomes be replicated during S phase?
DNA replication begins at many specific sites•
As the two DNA strands open at the origin, Replication Bubbles form
Prokaryotes (bacteria) have a single bubble
Eukaryotic chromosomes have MANY bubbles
3’
Parental DNA Molecule
5’ Replication
3’ Fork
5’
Origin of replication Parental strand
Daughter strand

Bubble
DNA Helicase
motor proteins that move directionally along a nucleic acid phosphodiester
backbone, separating two annealed nucleic acid strands using energy derived
from ATP hydrolysis
Helicase unwinds the double helix starting at a replication bubble.
The two strands separate as the hydrogen bonds between base pairs are broken.
Two replication forks form and the DNA is unwound in opposite directions.

Uses energy from ATP to

unwind the duplex DNA

SSB SSB

SSB SSB
SSB: Single-stranded DNA-binding Proteins
SSB Proteins
SSB: Single Stranded DNA-binding Proteins, bind to single-stranded regions
of DNA to prevent premature annealing, and to protect the single-stranded DNA
from being digested by nucleases.

Single-stranded DNA is produced during all aspects of DNA metabolism:

replication, recombination and repair
 Enzyme Enzyme
Topoisomerases
Topoisomerase: enzyme which relieves
stress on the DNA molecule by allowing
free rotation around a single strand.
DNA
DNA topoisomerase I
cut one strand of double-stranded DNA, relax the strand, and reanneal the strands
DNA topoisomerase II
cut both strands of the DNA helix simultaneously in order to manage DNA tangles
and supercoils. They use the hydrolysis of ATP, unlike type I topoisomerase
Starting DNA synthesis: RNA primers
RNA primer built by DNA primase serves as starter sequence for DNA
polymerase III

Before new DNA strands can form, there must be RNA primers present to start the
addition of new nucleotides

DNA polymerase III can only build onto 3

end of an existing DNA strand

In bacteria, primase binds to the DNA

helicase forming a complex called
the primosome. Primase is activated
by DNA helicase where it then synthesizes
a short RNA primer approximately 11 ± 1
nucleotides long, to which
new nucleotides can be added by DNA
polymerase.
DNA Synthesis by DNA polymerase
DNA polymerase III catalyzes the formation
of polynucleotide chains through the
addition of successive nucleotides derived
from deoxyribonucleoside triphosphates.
DNA polymerases III add nucleotides to the
3′ end of a polynucleotide chain. The
polymerase catalyzes the nucleophilic
attack of the 3′-hydroxyl group terminus of
the polynucleotide chain on the α-
phosphate group of the nucleoside
triphosphate to be added.
- To initiate this reaction, DNA polymerases
require a primer with a free 3′-hydroxyl
group already base-paired to
- Two metal ions (typically, Mg2+) participate in
the DNA polymerase reaction. One metal ion
coordinates the 3′-hydroxyl group of the primer,
whereas the phosphate group of the nucleoside
triphosphate bridges between the two metal ions.
The hydroxyl group of the primer attacks the
phosphate group to form a new O-P bond
Sliding clamp
A DNA clamp, also known as a sliding
clamp, is a protein fold that serves as
a processivity-promoting factor in DNA
replication.

As a critical component of the DNA

polymerase III , the clamp protein
binds DNA polymerase and prevents
this enzyme from dissociating from the
template DNA strand

the presence of the sliding clamp

dramatically increases the number
of nucleotides that can be added by
DNA polymerase
Because the rate-limiting step in the
DNA synthesis reaction is the
association of the polymerase with
the DNA template
The clamp-polymerase protein–protein interactions are stronger and more
specific than the direct interactions between the polymerase and the
template DNA strand
Leading strand is synthesized as a single polymer in the 5’ to 3’ direction

Leading Strand
5’ 3’
5’
RNA
Nucleotides DNA Polymerase
Primer

Lagging strand is also synthesized in the 5’ to 3’ direction but discontinuously

against the overall direction of replication

Series of short segments

on the lagging strand DNA
Okazaki Fragment Polymerase
RNA
Primer
5’ 3’

3’ 5’
Lagging Strand
Cycle of DNA Polymerase/Clamping Protein loading and
unloading at the lagging strand
Replication fork / Replication bubble

3 5

5 3

DNA polymerase III

leading strand
5
3 3 5
5 5
5 3 3
lagging strand

3 5
5
3 lagging strand leading strand
5 growing
3 replication fork 5
5 growing
replication fork 5
leading strand 3
lagging strand
3
5
5 5
Replacing RNA primers with DNA
Both Rnase H and DNA polymerase 1
remove sections of RNA primer and replaces with DNA nucleotides
But DNA polymerase I still can only build onto 3 end of an existing DNA strand

In the replication process, DNA Polymerase I and Rnase H removes

the RNA primer from the lagging strand and fills in the
necessary nucleotides between the Okazaki fragments in 5' - 3' direction,
proofreading for mistakes as it goes. It is a template-dependent enzyme - it only
adds nucleotides that correctly base pair with an existing DNA strand acting as a
template

DNA polymerase I 5

3

3
5 ligase
growing 3
replication fork
5

RNA 5

3
DNA Ligase
Finally the gaps in the sugar phosphate backbone are sealed by DNA ligase
Example: joining two Okazaki fragments together.
DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded
discontinuities in double stranded DNA molecules, in simple words strands that
have double-strand break (a break in both complementary strands of DNA)
The mechanism of DNA ligase is to form two covalent phosphodiester
bonds between 3' hydroxyl ends of one nucleotide, ("acceptor") with the 5'
phosphate end of another ("donor"). ATP is required for the ligase reaction,
which proceeds in three steps: (1) adenylation (addition of AMP) of a residue
in the active center of the enzyme, pyrophosphate is released; (2) transfer of
the AMP to the 5' phosphate of the so-called donor, formation of a
pyrophosphate bond; (3) formation of a phosphodiester bond between the 5'
phosphate of the donor and the 3' hydroxyl of the acceptor

There are now two identical double helices of DNA.

Energy of Replication
The nucleotides arrive as nucleosides
DNA bases with P–P–P
P-P-P = energy for bonding
DNA bases arrive with their own energy source for bonding
bonded by enzyme: DNA polymerase III

energy
energy

TTP
CTP
GTP
ATP CMP
TMP
ADP
GMP
AMP
modified nucleotide
What about the ends (or telomeres) of linear chromosomes?
Bacteria DNAs are circular, not a problem
There is a problem for eukaryote DNAs: ???
DNA polymerase/ligase cannot fill gap at end of chromosome after RNA primer
is removed. If this gap is not filled, chromosomes would become shorter
each round of replication!
DNA polymerase I
5

3

3
5
growing 3
replication fork DNA polymerase III
5

RNA 5

3

Solution:
special telomere sequence: tandem repeats of TTAGGG (human)
telomerase, a specific enzyme with integrated RNA template.
Telomeres

Repeating, non-coding sequences at the end of

chromosomes = protective cap
limit to ~50 cell divisions 

5

3

3
5
growing 3 telomerase
replication fork
5

5

TTAAGGG TTAAGGG 3

Telomerase
enzyme extends telomeres 
can add DNA bases at 5 end 
different level of activity in different cells 
 Step 1 = Binding

The binding-
polymerization- Step 2 = Polymerization
translocation cycle can
occurs many times

This greatly lengthens

one of the strands
Step 3 = Translocation

The complementary
strand is made by primase,
DNA polymerase and ligase

RNA primer
Initiation of replication, major elements:
Segments of single-stranded DNA are called template strands.

Gyrase (a type of topoisomerase) relaxes the supercoiled DNA.

Initiator proteins and DNA helicase binds to the DNA at the replication fork and
untwist the DNA using energy derived from ATP (adenosine triphosphate).
(Hydrolysis of ATP causes a shape change in DNA helicase)

DNA primase next binds to helicase producing a complex called a primosome

(primase is required for synthesis),

Primase synthesizes a short RNA primer of 10-12 nucleotides, to which DNA

polymerase III adds nucleotides.

Polymerase III adds nucleotides 5’ to 3’ on both strands beginning at the RNA

primer.

The RNA primer is removed and replaced with DNA by polymerase I, and the gap
is sealed with DNA ligase.

Single-stranded DNA-binding (SSB) proteins (>200) stabilize the single-stranded

template DNA during the process.
Editing & proofreading DNA
1000 bases/second =
lots of typos
DNA polymerase I
proofreads & corrects typos
repairs mismatched bases
removes abnormal bases
repairs damage
throughout life
reduces error rate from
1 in 10,000 to
1 in 100 million bases

During proofreading, DNA polymerase enzymes recognize this and replace the
incorrectly inserted nucleotide so that replication can continue. Proofreading
fixes about 99% of these types of errors, but that's still not good enough for
normal cell functioning.
After replication, mismatch repair reduces the final error rate even further.
Incorrectly paired nucleotides cause deformities in the secondary structure of
the final DNA molecule. During mismatch repair, enzymes recognize and fix
these deformities by removing the incorrectly paired nucleotide and replacing
it with the correct nucleotide
Types of DNA Damage
1- All four of the bases in DNA (A, T, C, G) can be covalently modified at
various positions.
One of the most frequent is the loss of an amino group ("deamination") —

resulting, for example, in a C being converted to a U.

2- Mismatches of the normal bases because of a failure of proofreading

during DNA replication.
Common example: incorporation of the pyrimidine U (normally found only
in RNA) instead of T.

3- Breaks in the backbone.

Can be limited to one of the two strands (a single-stranded break, SSB) or
on both strands (a double-stranded break (DSB).
Ionizing radiation is a frequent cause, but some chemicals produce
breaks as well.

4- Crosslinks Covalent linkages can be formed between bases

on the same DNA strand ("intrastrand") or
on the opposite strand ("interstrand").
Several chemotherapeutic drugs used against cancers crosslink DNA
Repairing Damaged Bases
Damaged or inappropriate bases can be repaired by several mechanisms:
Direct chemical reversal of the damage
Excision Repair, in which the damaged base or bases are removed and then
replaced with the correct ones in a localized burst of DNA synthesis. There are
three modes of excision repair, each of which employs specialized sets of
enzymes.
1-Base Excision Repair (BER)
2-Nucleotide Excision Repair (NER)
3-Mismatch Repair (MMR)
 Final Step - Assembly into
Nucleosomes:

As DNA unwinds, nucleosomes

must disassemble.

Histones and the associated

chromatin proteins must be
duplicated by new protein
synthesis.

Newly replicated DNA is

assembled into nucleosomes
almost immediately.

Histone chaperone proteins

control the assembly.

Addition of new histones

Chromatin assembly factors (CAFs)
help to add and assemble new
nucleosomes
A model for nucleosome replication
 DNA Replication ANIMATION
http://www.wiley.com/college/pratt/04713938
78/student/animations/dna_replication/ind
ex.html